You are using the default binding to $_ for the substitution without setting it. Also, the \Q\E pair in the replacement string are unwanted. Finally, the @pairs get overwritten with each iteration, which may or may not be OK depending on which string you want to modify. Assuming you want the replacement to be in @emotes,

#!/usr/bin/perl -w
use strict;

my $images_url = '/images';
my @emotes = <DATA>;
foreach my $entry (@emotes) {
    chomp $entry;
    my @pairs = split(/#####/, $entry);
    $entry =~ s/\Q$pairs[0]\E/<img src=\"$images_url\/emote_$pairs[1].
+gif\">/g;
}
print "@emotes",$/;

__DATA__
oX#####skullandbones
<;#####pie
(o)#####goatse
(~)#####ninja
[download]

I also arranged for the image url to be quoted.

After Compline,
Zaxo

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